The analysis of bacterial responses to environmental stimuli can provide valuable insights into cellular mechanisms (1-5). This approach is particularly well suited for studies of Mycobacterium tuberculosis, a pathogen that must adapt to a variety of hostile milieu including phagocytosis by macrophages and treatment with antibiotics. Differential gene expression in bacteria has been difficult to study because the absence of poly(A)+ RNA complicates removal of abundant ribosomal rRNA from low-abundance mRNA. The number of differentially expressed genes that have been identified in bacteria has been limited (6-11), except under circumstances where large amounts of RNA can be obtained (12). It recently has become possible to monitor gene expression in multiple bacterial genes simultaneously by direct hybridization of total RNA to high-density DNA arrays (12). However, the large amounts of labeled RNA that must be hybridized to such arrays currently restricts their utility in many biologically relevant investigations. This problem is not resolved by amplification of samples with the PCR because it often is not possible to amplify complex mixtures of mRNA sequences while at the same time maintaining their relative proportions (13). Accordingly, an efficient and rapid method of identifying differentially expressed mRNA would aid tremendously in understanding gene differential gene expression.
The existing need for an efficient and rapid method of identifying differentially expressed mRNA is met by the method provided by the present invention. The method provided by the present invention sets forth a novel combination of methods and principles which allows for the rapid and accurate isolation and identification of a large number of differentially expressed mRNAs.
Additional objects of the invention will be apparent from the description which follows.